> I have attached a new ChemDraw file with some generic structures in it. This
> raises the same error I have seen with the other files. I have also included
> a screenshot of the OpenBabel GUI conversion of the same .cdx file.
I have seen this before (e.g., inside of Avogadro or other programs) but have
not figured out what's different inside a Python script vs. the Open Babel
binaries themselves as far as the binary format reading.
As Noel, mentioned, please file a bug and we'll see what I can do.
One suggestion (albeit not a great one) is to use CDXML, which should read just
fine.
-Geoff
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